Thanks to David for reporting this. We can add the atom type to the list in pbsa. It's the new C-alpha.
Best,
Qin
On Mar 17, 2012, at 7:33 PM, Ray Luo, Ph.D. wrote:
> I'm forwarding this to Qin for an answer ...
>
> Ray
>
>
> ---------- Forwarded message ----------
> From: David Minh <daveminh.gmail.com>
> Date: Sat, Mar 17, 2012 at 11:10 AM
> Subject: [AMBER] PB with inp=2 doesn't recognize ff10 atom types?
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Hi Amber folk,
>
> After running a pmemd.cuda simulation on a normal protein prepared
> with tleap and leaprc.ff10, I tried to run a PBSA calculation with
> inp=2 using sander in AMBER 11 with the script on the bottom of this
> email. However, I got the error,
>
> PB Bomb in pb_aaradi(): No radius assigned for atom 5 CA CX
>
> This had me stuck for a little bit, but then I used leaprc.ff99SB in
> tleap to generate the prmtop instead. It worked perfectly and I had
> the same MM energies as with a GB script and the original prmtop.
>
> I am just writing the list to provide a workaround in case somebody
> else runs into this problem, and also to alert developers to the
> possibility that PB with inp=2 might not support ff10 atom types with
> different names than ff99SB (if they don't already know).
>
> Thanks,
> David
>
> ** Example sander energies given the prmtop based on ff10:
>
> minimizing coord set # 2
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -3.2302E+03 1.9446E+01 1.0836E+02 CG 2052
>
> BOND = 398.8477 ANGLE = 1119.9287 DIHED = 1505.8676
> VDWAALS = -1035.4726 EEL = -9542.4883 EGB = -2005.0136
> 1-4 VDW = 522.2311 1-4 EEL = 5805.9078 RESTRAINT = 0.0000
> minimization completed, ENE= -.32301916E+04 RMS= 0.194458E+02
>
> ** Example sander energies given the prmtop based on ff99SB
>
> minimizing coord set # 2
>
>
> Maximum number of minimization cycles reached.
>
>
> FINAL RESULTS
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.6930E+03 1.9490E+01 1.0846E+02 CG 2052
>
> BOND = 398.8477 ANGLE = 1119.9287 DIHED = 1505.8676
> VDWAALS = -1035.4726 EEL = -9542.4883 EPB = -1894.4982
> 1-4 VDW = 522.2311 1-4 EEL = 5805.9078 RESTRAINT = 0.0000
> ECAVITY = 1144.2085 EDISPER = -717.5027
> minimization completed, ENE= -.26929704E+04 RMS= 0.194899E+02
>
> ** GB script:
>
> Calculate GB energies
> &cntrl
> imin=5, maxcyc=0, ncyc=0, ! read trajectory in for analysis
> ntx=1, ! input is read formatted with no velocities
> ntb=0, ! no periodicity and no PME
> idecomp=0, ! no decomposition
> ntc=2, ! SHAKE
> ntf=2, ! omit interactions with H-atoms
> cut=1000.0, ! no cutoff (>999.0)
> nsnb=99999, ! don't update non-bonded list
> temp0=300.0, ! 300 K
> igb=5, ! Updated OBC implicit solvent
> saltcon=0.025, ! 25 mM salt
> ioutfm=1, ! Binary NetCDF output
> /
>
> ** PBSA script:
>
> Calculate Poisson-Boltzmann energies
> &cntrl
> imin=5, maxcyc=0, ncyc=0, ! read trajectory in for analysis
> ntx=1, ! input is read formatted with no velocities
> ntb=0, ! no periodicity and no PME
> idecomp=0, ! no decomposition
> ntc=2, ! SHAKE
> ntf=2, ! omit interactions with H-atoms
> cut=1000.0, ! no cutoff (>999.0)
> nsnb=99999, ! don't update non-bonded list
> temp0=300.0, ! 300 K
> ipb=2, ! PBSA
> inp=2, ! Two terms for nonpolar solvation energy
> ioutfm=1, ! Binary NetCDF output
> /
> &pb
> istrng=25, ! 25 mM salt
> pbtemp=300.0, ! 300 K
> epsout=80.0, epsin=1.0,
> radiopt=1, ! use radii (missing parameter from terminal residue?)
> dprob=1.6,
> space=0.5, nbuffer=0, fillratio=4.0,
> accept=0.001,
> cutnb=0, eneopt=2,
> decompopt=2, ! sigma decomposition scheme (Luo's paper)
> use_rmin=1, ! use van der Waals rmin values
> sprob=0.557, ! recommended for sigma decomposition scheme
> vprob=1.300,
> rhow_effect=1.129, ! recommended for sigma decomposition scheme
> use_sav=1, ! use molecular volume enclosed by SASA
> cavity_surften=0.0378, ! recommended by Luo
> cavity_offset=-0.5692, ! recommended by Luo
> /
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Received on Mon Mar 19 2012 - 15:30:03 PDT
